mtDNAmanager: Updates for generating high-quality mitochondrial DNA - - PDF document

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Updates for generating high-quality mitochondrial DNA data from a phylogenetic perspective

Hwan Young Lee, Woo Ick Yang, Kyoung-Jin Shin Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea

mtDNAmanager: Outline

• The first release of mtDNAmanager in 2007

Background Aims Implementation

• Recent updates

Database expansion Refinement of control region mutation motifs

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Background

• Mitochondrial DNA (mtDNA) typing is more prone to human

error than other forensic DNA analysis

• Errors were mainly due to misinterpretation of sequence raw

data and due to the introduction of clerical errors during data transcription

• Phylogenetic investigations and database screening

could have detected prevalent errors in published datasets (e.g., Bandelt et al. Science 2004, 305:1402)

• Attempts to localize the sequence to a part of phylogeny

(haplogroup). If the haplogroup motif is not fully represented, recheck the relevant positions in the sequence

• Have in mind the relative mutability of sites. Be sensitive to

rare mutations on different sequence backgrounds in one batch of sequencing

• Look out for incongruence between parts of the sequences

which have been obtained in different PCR or sequencing reactions (artificial recombinants)

How to avoid mtDNA sequence errors

Bandelt et al. IJLM (2001) 115:64-9

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• Methodologies

based

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mtDNA haplogroup determination and comparisons with existing mtDNA haplotypes were proposed for preventing mtDNA errors

• Manual haplogroup

estimation requires a thorough understanding of the worldwide mtDNA phylogeny

• Database screening for systematic error detection requires

high-quality databases that are publicly available

Need for software development http://mtmanager.yonsei.ac.kr mtDNAmanager’s first release in 2007

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Worldwide access to mtDNAmanager

Since its first release in 2007, the mtDNAmanager has been accessed by users from 75 nations more than 13,000 times

Monthly access to mtDNAmanager

Number of access Number of visitors Rate of newcomers : Revisit 66.22%

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• To allow researchers to automatically estimate the most-

probable mtDNA haplogroups of their mtDNA control region sequences

• To facilitate database screening with improved query tools
• To provide researchers with a convenient interface for

managing and analyzing their own data in batch mode

Aims of mtDNAmanager

• The mtDNAmanager

interface was designed to allow researchers to easily query the database and immediately view the results on a single page

• The mtDNAmanager's first release contained 4839 mtDNA

control region sequences from FBI and 593 Korean mtDNA control region sequences and a set of bioinformatics tools able to automatically characterize newly submitted data by estimating its most-probable mtDNA haplogroup based on more than 350 haplogroup-specific control region mutation motifs.

Design and content of mtDNAmanager

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• The phased designation of haplogroups (i.e. expected haplogroup and estimated

haplogroup) suggests candidate sites that need reinvestigation by allowing the respective confirmation of the presence of clear diagnostic mutations and accompanying mutations.

The most-probable haplogroup estimation

150?

N9a3: 16129-16223-16257A-16261-150

16319 missed

• ut?

A5a: 16187-16223-16290-16319-235-523d-524d

Database search using query system

• A query system retrieves sequences that include queried nucleotide polymorphisms

from a selected database or the entire population group of its open database. Include setting Estimated mtDNA haplogroup affiliations using the bioinformatics resources of the mtDNAmanager Target database

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Database search using query system

• With the alternative setting of match, the mtDNAmanager also searches sequences that

match the queried sequence data from the database. Frequency estimates = (x+2)/(n+2) Match setting Target database

A sample system

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A match system A query system

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• The number of mtDNA control region sequences in

the mtDNAmanager’s open database has grown from 5,432 to 9,180, while the number of population groups has been increased to more than 20.

• The number of control region mutation motifs for the

assignment of the most-probable mtDNA haplogroups has grown from 350 to more than 590.

Updates from the first release

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mtDNAmanager’s current open database

20 more publications were added

Expansion of mtDNAmanager’s database

DB at 1st release Current DB

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Improved database search Recent updates in phylogenetic trees

African: L0~L5 South East Asian: ~M71, M72 South Asian: M31, M33, M51… PhyloTree.org

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Control Region Mutation motif for more than 590 mtDNA haplogroups

• Refinement of mtDNA phylogeny with more diagnostic mutations would facilitate the

detection of more errors in mtDNA sequence since it is based on mutation motifs

Improved mtDNA haplogroup estimation

Added mutation motifs enables refined mtDNA haplogroup estimation

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• Refinement of mtDNA phylogeny with more diagnostic

mutations would provide better algorithms for automatic estimation of the most-probable mtDNA haplogroups in diverse population groups, and facilitate the detection of more errors in mtDNA sequence data by suggesting more candidate sites for reinvestigation

• A neighbourhood

search for sequences in the expanded open database would facilitate pinpointing errors through extensive data comparison using the expanded subset of the total database

Updates in mtDNAmanager

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Concluding remarks

• With these improvements mtDNAmanager will help in

checking the quality

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data and facilitate data comparisons from a phylogenetic perspective

• Continuous efforts are needed to collect and integrate

high-quality mtDNA control region sequence data for various population groups in South East Asia and Oceania

For comments, bug reports, suggestions for improvement, please contact us through the website (http://mtmanager.yonsei.ac.kr).